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Pipeline publication

[…] software package of CLSM 510 META and Adobe Photoshop CS., Three-dimensional (3D) model of plant kinesin-8 was constructed on the online server SwissModel Workspace (Arnold et al., ) using the A. thaliana primary sequence (UniProtKB/TrEMBL code: Q9FZ77) and 3LRE crystal of human kinesin-8 motor domain KIF18A (Peters et al., ) as a matrix. The full 3D models of α-and β-tubulins from A. thaliana were constructed using the online server I-TASSER on the basis of primary sequences P11139 and P12411, respectively (Blume et al., ). Overlay of the constructed molecules of A. thaliana kinesin-8, α- and β-tubulins with the appropriated structures from 1IA0 crystal (Kikkawa et al., ) was performed in Swiss-PdbViewer 4.1.0 software package. Alteration of C-terminal region position of plant α-tubulin and Tyr450 modifications were simulated in the Discovery Studio 3.5 Visualizer company Accelrys© software package., The optimization of the molecular geometry of the constructed models, molecular dynamics simulation of protein-protein complex and analysis of the results were performed using the specialized modules from Gromacs 4.5.4 software package (Hess et al., ; Pronk et al., ). Topology data for the unnatural amino acid used for charmm27 force field was obtained from the database SwissSidechain (Gfeller et al., ). In order to reproduce the intracellular environment, protein complexes were immersed in water and its volume was determined by the size of the studied macromolecules. Distant electrostatic interactions were calculated by PME method (Particle Mesh Ewald) (Essmann et al., ). As one of the conditions of its use for the calculation of the Coulomb interactions is the neutral system status, the nonzero charges of the obtained systems were neutralized by the automatic substitution of random water molecules with sodium and chlorine ions, which amount corresponded to physiological concentration (0.15 mol/L). Optimi […]

Pipeline specifications

Software tools Swiss-PdbViewer, GROMACS, CHARMM
Databases UniProtKB SwissSidechain
Organisms Arabidopsis thaliana, Nicotiana tabacum
Chemicals Nitric Oxide, Oxides, Reactive Nitrogen Species